Histone modifications play an essential role in chromatin-associated processes including gene regulation and epigenetic inheritance. It is therefore very important to quantitatively analyze histone modifications at both the single gene and whole genome level. Here, we describe a robust chromatin immunoprecipitation (ChIP) method for Arabidopsis, which could be adapted for other plant species. This method is compatible with multiple downstream applications including qPCR, tilling arrays, and high-throughput sequencing.